论文标题

我的网络距离基于边缘有多远?基于边缘的系统发育网络基于边缘的接近度度量

How far is my network from being edge-based? Proximity measures for edge-basedness of unrooted phylogenetic networks

论文作者

Fischer, Mareike, Hamann, Tom Niklas, Wicke, Kristina

论文摘要

与树木相反,适合描述诸如杂交和水平基因转移等过程的系统发育网络在进化研究中起着重要作用。但是,尽管需要考虑非真实事件,但它们相对较少,这意味着通常认为与树木相似的网络在某种意义上可以通过取树并添加一些额外的边缘来获得树木相似。这一观察结果导致了所谓的基于树的网络的概念,该网络最近对文献引起了重大兴趣。但是,不幸的是,在未根除的情况下识别此类网络是NP完整的问题。因此,可以保证基于树的网络的类别具有最大的兴趣。 最突出的类别是由所谓的基于边缘的网络形成的,这些网络与图理论已知的广义串联平行图具有密切的关系。它们可以在线性时间内识别,并且在某些方面比一般基于树的网络更合理。尽管已经引入了有关通用网络的后一种接近度度量,但此类措施尚未用于基于边缘的度量。这意味着,对于任意无根备的网络,到目前为止无法确定基于边缘网络的“距离”。本手稿通过引入基于边缘的两类接近度度量来填补这一空白,这是基于给定的网络本身,另一类基于其所谓的叶收缩图(LS图)。这两个类别都包含四种不同的接近度度量,我们随后研究它们的相似性和差异。

Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into account, they are relatively rare, which implies that biologically relevant networks are often assumed to be similar to trees in the sense that they can be obtained by taking a tree and adding some additional edges. This observation led to the concept of so-called tree-based networks, which recently gained substantial interest in the literature. Unfortunately, though, identifying such networks in the unrooted case is an NP-complete problem. Therefore, classes of networks for which tree-basedness can be guaranteed are of the utmost interest. The most prominent such class is formed by so-called edge-based networks, which have a close relationship to generalized series-parallel graphs known from graph theory. They can be identified in linear time and are in some regards biologically more plausible than general tree-based networks. While concerning the latter proximity measures for general networks have already been introduced, such measures are not yet available for edge-basedness. This means that for an arbitrary unrooted network, the "distance" to the nearest edge-based network could so far not be determined. The present manuscript fills this gap by introducing two classes of proximity measures for edge-basedness, one based on the given network itself and one based on its so-called leaf shrink graph (LS graph). Both classes contain four different proximity measures, whose similarities and differences we study subsequently.

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